[med-svn] [infernal] branch upstream updated (0d174cd -> b52cde2)
Sascha Steinbiss
satta at debian.org
Sat Aug 6 01:23:21 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch upstream
in repository infernal.
from 0d174cd Imported Upstream version 1.1.1
new b52cde2 Imported Upstream version 1.1.2
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
COPYRIGHT | 46 -
INSTALL | 37 +-
LICENSE | 731 +-
Makefile.in | 25 +-
README | 19 +-
RELEASE-NOTES | 192 +-
Userguide.pdf | Bin 925365 -> 905189 bytes
aclocal.m4 | 874 +-
configure | 1292 +-
configure.ac | 47 +-
documentation/Makefile.in | 4 +-
documentation/manpages/Makefile.in | 4 +-
documentation/manpages/cmalign.man | 6 +-
documentation/manpages/cmbuild.man | 6 +-
documentation/manpages/cmcalibrate.man | 6 +-
documentation/manpages/cmconvert.man | 6 +-
documentation/manpages/cmemit.man | 6 +-
documentation/manpages/cmfetch.man | 6 +-
documentation/manpages/cmpress.man | 6 +-
documentation/manpages/cmscan.man | 90 +-
documentation/manpages/cmsearch.man | 8 +-
documentation/manpages/cmsearch_dual.man | 6 +-
documentation/manpages/cmstat.man | 6 +-
documentation/manpages/infernal.man | 6 +-
documentation/manpages/sse_cmsearch.man | 6 +-
documentation/userguide/Makefile.in | 13 +-
documentation/userguide/ack.tex | 5 +-
documentation/userguide/cmbuild.tex | 5 +-
documentation/userguide/copyright.tex | 0
documentation/userguide/copyright.tex.in | 18 -
documentation/userguide/formats.tex | 43 +-
documentation/userguide/install.tex | 24 +-
documentation/userguide/introduction.tex | 8 +-
documentation/userguide/main.tex | 8 +-
documentation/userguide/more.tex | 21 +-
documentation/userguide/pipeline.tex | 3 +-
documentation/userguide/tabular.tex | 151 +-
documentation/userguide/titlepage.tex.in | 9 +-
documentation/userguide/tutorial.tex | 282 +-
easel/00README | 12 +-
easel/BUGTRAX | 51 +-
easel/COPYRIGHT | 27 -
easel/INSTALL | 10 +-
easel/LICENSE | 86 +-
easel/Makefile.in | 107 +-
easel/aclocal.m4 | 711 +-
easel/config.guess | 0
easel/config.sub | 0
easel/configure | 3972 +-
easel/configure.ac | 228 +-
easel/demotic/demotic_blast.pm | 11 +-
easel/demotic/demotic_fasta.pm | 161 +-
easel/demotic/demotic_hmmer.pm | 33 +-
easel/demotic/infernal_tab2gff.pl | 0
easel/demotic/test.pl | 0
easel/devkit/autodoc | 17 +-
easel/devkit/cexcerpt | 0
easel/devkit/sqc | 74 +-
easel/documentation/Makefile.in | 29 +-
easel/documentation/codestyle.tex | 427 +-
easel/documentation/copyright.tex | 9 +-
easel/documentation/intro.tex | 130 +-
easel/documentation/macros.tex | 20 +-
easel/documentation/main.tex | 176 +-
easel/documentation/titlepage.tex | 14 +-
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easel/easel.h | 107 +-
easel/esl_alphabet.c | 183 +-
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easel/esl_avx.h | 113 +
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easel/esl_composition.c | 150 +
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easel/esl_dmatrix.h | 27 +-
easel/esl_dsqdata.c | 1700 +
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easel/esl_fileparser.c | 169 +-
easel/esl_fileparser.h | 14 +-
easel/esl_gamma.c | 370 +-
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easel/esl_msafile.md | 181 +
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easel/esl_msafile_a2m.c | 179 +-
easel/esl_msafile_a2m.h | 19 +-
easel/esl_msafile_afa.c | 200 +-
easel/esl_msafile_afa.h | 19 +-
easel/esl_msafile_clustal.c | 198 +-
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easel/esl_msafile_phylip.c | 501 +-
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easel/esl_vectorops.c | 69 +-
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hmmer/src/p7_hmmfile.c | 91 +-
hmmer/src/p7_hmmwindow.c | 34 +-
hmmer/src/p7_msvdata.c | 421 -
hmmer/src/p7_null3.c | 123 +-
hmmer/src/p7_pipeline.c | 906 +-
hmmer/src/p7_prior.c | 35 +-
hmmer/src/p7_profile.c | 8 +-
hmmer/src/p7_scoredata.c | 465 +
hmmer/src/p7_spensemble.c | 2 +-
hmmer/src/p7_tophits.c | 366 +-
hmmer/src/p7_trace.c | 6 +-
hmmer/src/phmmer.c | 358 +-
hmmer/src/seqmodel.c | 8 +-
hmmer/src/tracealign.c | 81 +-
hmmer/testsuite/2OG-FeII_Oxy_3-nt.hmm | 968 +
hmmer/testsuite/2OG-FeII_Oxy_3.hmm | 327 +
hmmer/testsuite/Makefile.in | 8 +-
hmmer/testsuite/i10-duplicate-names.pl | 2 +-
hmmer/testsuite/i11-hmmalign-mapali.pl | 2 +-
hmmer/testsuite/i12-delete-corruption.pl | 2 +-
hmmer/testsuite/i13-msa-integrity.pl | 2 +-
hmmer/testsuite/i17-stdin.pl | 2 +-
hmmer/testsuite/i18-nhmmer-generic.pl | 48 +-
hmmer/testsuite/i20-fmindex-core.pl | 2 +-
hmmer/testsuite/i9-optional-annotation.pl | 2 +-
hmmer/testsuite/testsuite.sqc | 100 +-
hmmer/tutorial/MADE1.hmm | 265 +
hmmer/tutorial/MADE1.out | 118 +
hmmer/tutorial/MADE1.sto | 4021 ++
hmmer/tutorial/SNORD96.hmm | 313 -
hmmer/tutorial/SNORD96.out | 82 -
hmmer/tutorial/SNORD96.sto | 16 -
hmmer/tutorial/dna_target.fa | 42680 +++----------------
hmmer/tutorial/fn3.hmm | 177 +-
hmmer/tutorial/fn3.out | 38 +-
hmmer/tutorial/globins4.hmm | 303 +-
hmmer/tutorial/globins4.out | 7489 ++--
hmmer/tutorial/minifam.h3f | Bin 54780 -> 54792 bytes
hmmer/tutorial/minifam.h3m | Bin 96927 -> 96927 bytes
hmmer/tutorial/minifam.h3p | Bin 113252 -> 113765 bytes
rmark/Makefile.in | 4 +-
rmark/rmark-create.c | 186 +-
src/Makefile.in | 4 +-
src/Rfam.12.1.claninfo | 104 +
src/alphabet.c | 2 +-
src/bandcyk-montecarlo-test.c | 6 +-
src/bandcyk-truncation-test.c | 9 +-
src/cm.c | 36 +-
src/cm_alidisplay.c | 6 +-
src/cm_alndata.c | 2 +-
src/cm_dispatch.h | 4 +-
src/cm_dpalign.c | 23 +-
src/cm_dpalign_trunc.c | 12 +-
src/cm_dpsearch.c | 26 +-
src/cm_dpsearch_trunc.c | 16 +-
src/cm_dpsmall.c | 6 +-
src/cm_file.c | 16 +-
src/cm_modelconfig.c | 6 +-
src/cm_modelmaker.c | 12 +-
src/cm_mx.c | 60 +-
src/cm_p7_modelmaker.c | 7 +-
src/cm_parsetree.c | 7 +-
src/cm_pipeline.c | 681 +-
src/cm_qdband.c | 6 +-
src/cm_submodel.c | 14 +-
src/cm_tophits.c | 1537 +-
src/cm_trunc.c | 2 +-
src/cmalign.c | 103 +-
src/cmbuild.c | 46 +-
src/cmcalibrate.c | 35 +-
src/cmconvert.c | 4 +-
src/cmemit.c | 8 +-
src/cmfetch.c | 4 +-
src/cmpress.c | 4 +-
src/cmscan.c | 1572 +-
src/cmsearch.c | 257 +-
src/cmstat.c | 4 +-
src/config.h.in | 2 +-
src/cp9-test.c | 4 +-
src/cp9.c | 4 +-
src/cp9_dp.c | 4 +-
src/cp9_modelmaker.c | 9 +-
src/cp9_trace.c | 10 +-
src/display.c | 6 +-
src/eweight.c | 6 +-
src/hmmband.c | 23 +-
src/hmmband.h | 4 +-
src/impl_sse/Makefile.in | 4 +-
src/impl_sse/impl_sse.h | 4 +-
src/impl_sse/sse_cm_dpsearch.c | 14 +-
src/impl_sse/sse_cm_dpsmall.c | 18 +-
src/impl_sse/sse_cmcons_hitmx.c | 6 +-
src/impl_sse/sse_cmcons_mscyk.c | 4 +-
src/infernal.h | 86 +-
src/mpisupport.c | 27 +-
src/prior.c | 2 +-
src/prior.h | 2 +-
src/sa-Makefile.in | 4 +-
src/sub_cm-test.c | 4 +-
src/trcyk.c | 2 -
testsuite/{4.c.cm => 5.c.cm} | 701 +
testsuite/5.claninfo | 1 +
testsuite/Makefile.in | 4 +-
testsuite/Rfam.12.1.clanin | 104 +
testsuite/bug-i1.pl | 2 +-
testsuite/bug-i38.pl | 2 +-
testsuite/bug-i44.pl | 82 +
testsuite/dev_testsuite.sqc | 23 +-
testsuite/emitted-5.fa | 19 +
testsuite/i1.pm | 81 +-
testsuite/itest2-duplicate-names.pl | 4 +-
testsuite/itest5-pipeline.pl | 8 +-
testsuite/itest6-sensitivity.pl | 16 +-
testsuite/itest7-trunc.pl | 24 +-
testsuite/itest8-glist.pl | 6 +-
testsuite/itest9-overlaps.pl | 174 +
testsuite/tRNA-Sec.c.cm | 701 +
testsuite/testsuite.sqc | 6 +
tutorial/tRNA5.c.cm | 14 +-
570 files changed, 56664 insertions(+), 64285 deletions(-)
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create mode 100644 hmmer/documentation/man/hmmpgmd.man
create mode 100644 hmmer/documentation/man/makehmmerdb.man
create mode 100644 hmmer/documentation/man/nhmmer.man
copy hmmer/documentation/man/{hmmscan.man => nhmmscan.man} (63%)
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delete mode 100644 hmmer/src/fm_msv.c
rename hmmer/src/{impl_sse/fm.c => fm_sse.c} (68%)
create mode 100644 hmmer/src/fm_ssv.c
rename hmmer/src/{exactmatch.c => hmmerfm-exactmatch.c} (65%)
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rename hmmer/src/{makenhmmerdb.c => makehmmerdb.c} (60%)
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create mode 100644 hmmer/testsuite/2OG-FeII_Oxy_3-nt.hmm
create mode 100644 hmmer/testsuite/2OG-FeII_Oxy_3.hmm
create mode 100644 hmmer/tutorial/MADE1.hmm
create mode 100644 hmmer/tutorial/MADE1.out
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copy testsuite/{4.c.cm => 5.c.cm} (85%)
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create mode 100644 testsuite/tRNA-Sec.c.cm
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